کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10231947 | 1423 | 2005 | 7 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Haplotype assembly from aligned weighted SNP fragments
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کلمات کلیدی
موضوعات مرتبط
مهندسی و علوم پایه
مهندسی شیمی
بیو مهندسی (مهندسی زیستی)
پیش نمایش صفحه اول مقاله
![عکس صفحه اول مقاله: Haplotype assembly from aligned weighted SNP fragments Haplotype assembly from aligned weighted SNP fragments](/preview/png/10231947.png)
چکیده انگلیسی
Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211-213)). In this paper we show that the general WMLF model is NP-hard even for the gapless case. However the algorithmic solutions for selected variants of WMFL can exist and we propose a heuristic algorithm based on a dynamic clustering technique. We also introduce a new formulation of the haplotype assembly problem that we call COMPLETE WMLF (CWMLF). This model and algorithms for its implementation take into account a simultaneous presence of multiple kinds of data errors. Extensive computational experiments indicate that the algorithmic implementations of the CWMLF model achieve higher accuracy of haplotype reconstruction than the WMLF-based algorithms, which in turn appear to be more accurate than those based on MLF.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computational Biology and Chemistry - Volume 29, Issue 4, August 2005, Pages 281-287
Journal: Computational Biology and Chemistry - Volume 29, Issue 4, August 2005, Pages 281-287
نویسندگان
Yu-Ying Zhao, Ling-Yun Wu, Ji-Hong Zhang, Rui-Sheng Wang, Xiang-Sun Zhang,